Age-Dependent Hippocampal Proteomics in the APP/PS1 Alzheimer Mouse Model: A Comparative Analysis with Classical SWATH/DIA and directDIA Approaches

Abstract

Alzheimer’s disease (AD) is the most common neurodegenerative disorder in the human population, for which there is currently no cure. The cause of AD is unknown; however, the toxic effects of amyloid-β (Aβ) are believed to play a role in its onset. To investigate this, we examined changes in global protein levels in a hippocampal synaptosome fraction of the Amyloid Precursor Protein swe/Presenelin 1 dE9 (APP/PS1) mouse model of AD at 6 and 12 months of age (moa). Data independent acquisition (DIA), or Sequential Window Acquisition of all THeoretical fragment-ion (SWATH), was used for a quantitative label-free proteomics analysis. We first assessed the usefulness of a recently improved directDIA workflow as an alternative to conventional DIA data analysis using a project-specific spectral library. Subsequently, we applied directDIA to the 6- and 12-moa APP/PS1 datasets and applied the Mass Spectrometry Downstream Analysis Pipeline (MS-DAP) for differential expression analysis and candidate discovery. We observed most regulation at 12-moa, in particular of proteins involved in Aβ homeostasis and microglial-dependent processes, like synaptic pruning and the immune response, such as APOE, CLU and C1QA-C. All proteomics data are available via ProteomeXchange with identifier PXD025777.

The amyloid peptide β disrupts intercellular junctions and increases endothelial permeability in a NADPH oxidase 1-dependent manner

“…Similarly to our study, cytoskeletal integrity, mitochondrial function, protein turnover and cell signalling were the cellular functions more heavily affected. Other recent proteomics studies on the hippocampus of the APP/PS1 mouse model of AD show similarities with our results, with changes in proteins involved in protein turnover pathways (both synthesis and degradation) [ 52 , 53 ], neurotransmission [ 52 ], and, importantly, oxidative stress [ 53 ]. A key result of our proteomics study is in fact the identification of expression changes for proteins and enzymes associated with redox homeostasis, which suggests the possibility that the brain accumulation of amyloid peptide β leads to oxidative stress.…”

Activity-dependent translation dynamically alters the proteome of the perisynaptic astrocyte process

“…Samples were loaded onto an Ultimate 3000 LC system (Dionex, Thermo Scientific) as described ( Gonzalez-Lozano et al, 2020 ; Hondius et al, 2021 ; van der Spek et al, 2021 ). A generally used hippocampal synaptosomes library created in-house with MaxQuant Software was used to annotate proteins.…”

Small extracellular vesicles derived from dermal fibroblasts promote fibroblast activity and skin development through carrying miR-218 and ITGBL1

“…The SEV protein was digested using a filter-aided sample preparation method [ 45 ]. The polypeptide was obtained and analysed by reversed-phase liquid chromatography-tandem mass spectrometry (RPLC–MS/MS).…”